|
| Status |
Public on Nov 01, 2021 |
| Title |
MDR CIBIN:UMF:15:99 UCI-05 rep1 |
| Sample type |
RNA |
| |
|
| Source name |
RNA from M. tuberculosis, CIBIN:UMF:15:99 clone 1 treated with UCI-05
|
| Organism |
Mycobacterium tuberculosis H37Rv |
| Characteristics |
drug resistance: MDR
replicate: MDR biological rep 1 treated with UCI-05
|
| Treatment protocol |
Each clone culture was treated with compound 1, 2 (at a final concentration equivalent to their respective MICs) or 0.1% DMSO (as control) and incubated under the same conditions for additional 4 h.
|
| Growth protocol |
1.0 mL of McF 1 inoculum was growth in 10 mL Middlebrook 7H9 medium supplemented with 10% OADC and incubated at 37 °C in 5% CO2 atmosphere with constant shaking (at 300 rpm) until mycobacteria reached growth log phase
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent and the Fast Prep instrument.
|
| Label |
Biotin
|
| Label protocol |
The cDNA was fragmented with DNaseI and labeled at the 3' termini using 60U of Terminal Deoxynucleotidyl Transferase and 7.5 mM biotinylated GeneChip DNA Labeling Reagent.GeneChip DNA Labeling Reagent
|
| |
|
| Hybridization protocol |
The labeled cDNA product was heated to 95°C and hybridized to the Affymetrix GeneChip TB-All Antisense microarrays for 17 h at 45°C.
|
| Scan protocol |
Fluorescent signal was measured and the Affymetrix GeneChip Expression Console was used to obtain the intensity signal and quality control data of the scanned arrays.
|
| Description |
Gene expression data of MDR-MTB clone treated with compund 1
|
| Data processing |
Microarray data was pre-processed using the MAS5 algorithm. Raw intensity values were background-corrected, log2-transformed, and then quantile-normalized. A linear model using the limma package was fit to the normalized data to identify differential expression
|
| |
|
| Submission date |
Sep 15, 2021 |
| Last update date |
Nov 01, 2021 |
| Contact name |
Katia Penuelas-Urquides |
| Organization name |
Instituto Mexicano del Seguro Social
|
| Department |
Molecular Biology Dept.
|
| Lab |
Molecular Microbiology
|
| Street address |
Calle 2 de abril 501, Col. Independencia
|
| City |
Monterrey |
| State/province |
Nuevo León |
| ZIP/Postal code |
64720 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL4519 |
| Series (1) |
| GSE184172 |
ANALYSIS OF THE GENETIC EXPRESSION PROFILES OF SENSITIVE AND MULTIPHARMACORRESISTANT Mycobacterium tuberculosis CLONES EXPOSED TO NEW COMPOUNDS |
|
